Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007923.1 Hibiscus syriacus cultivar Beakdansim tig00110328_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8415618
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 40
Found at i:1860324 original size:184 final size:184
Alignment explanation
Indices: 1860037--1860378 Score: 571
Period size: 184 Copynumber: 1.9 Consensus size: 184
1860027 TGTAACAATA
* * *
1860037 AGGAACTACTTTCCGGTTGAAGTTTAAACTGAGGTCTTTAAGTCAAGAAGAAGACCTGGGTTGGT
1 AGGAACTACTTTCCGGTTAAAGTTTAAACTGAGGTCTTTAAGTCAAGAAGAAGACCTGAGTTGGC
* * *
1860102 TGCGATTTAGCAATAAGGAACTATATCTCATCCAAATTTACAACATAGCTCAAGGTGAGAAGGAC
66 TACGATTTAGCAACAAGGAACTATATCTCATCCAAATTTACAACATAGCTCAAGGCGAGAAGGAC
*
1860167 TATCTTTCAACGAAAAACTTTCGAGTTCAACATGTCAACCGCACTGTAGCAGCG
131 TATCTATCAACGAAAAACTTTCGAGTTCAACATGTCAACCGCACTGTAGCAGCG
1860221 AGGAACTACTTTCCGGTTAAAGTTTAAACTGAGGTCTTTAAGTCAAGAAGAAGACCTGAGTTGGC
1 AGGAACTACTTTCCGGTTAAAGTTTAAACTGAGGTCTTTAAGTCAAGAAGAAGACCTGAGTTGGC
*
1860286 TACGATTTAGCAACAAGGAGCTATATC-CTAGT-CAAATTTACAACATAGCTCAAGGCGAGAAGG
66 TACGATTTAGCAACAAGGAACTATATCTC-A-TCCAAATTTACAACATAGCTCAAGGCGAGAAGG
*
1860349 GCTATCTATCAACGAAAAACTTTCGAGTTC
129 ACTATCTATCAACGAAAAACTTTCGAGTTC
1860379 GATTCCATTC
Statistics
Matches: 147, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
183 1 0.01
184 145 0.99
185 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (184 bp):
AGGAACTACTTTCCGGTTAAAGTTTAAACTGAGGTCTTTAAGTCAAGAAGAAGACCTGAGTTGGC
TACGATTTAGCAACAAGGAACTATATCTCATCCAAATTTACAACATAGCTCAAGGCGAGAAGGAC
TATCTATCAACGAAAAACTTTCGAGTTCAACATGTCAACCGCACTGTAGCAGCG
Found at i:1861039 original size:37 final size:38
Alignment explanation
Indices: 1860997--1861075 Score: 110
Period size: 38 Copynumber: 2.1 Consensus size: 38
1860987 AATTATATAG
1860997 TATAATTTTT-GAAAAC-ATT-TTCGAAAAACATATAACA
1 TATAATTTTTAGAAAACGATTATT--AAAAACATATAACA
*
1861034 TATAATTTTTAGAAAACGATTATTAAAAACATATAATA
1 TATAATTTTTAGAAAACGATTATTAAAAACATATAACA
1861072 TATA
1 TATA
1861076 CTTTAAAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
37 10 0.26
38 23 0.61
39 3 0.08
40 2 0.05
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.37
Consensus pattern (38 bp):
TATAATTTTTAGAAAACGATTATTAAAAACATATAACA
Found at i:1861146 original size:36 final size:37
Alignment explanation
Indices: 1861094--1861172 Score: 115
Period size: 36 Copynumber: 2.1 Consensus size: 37
1861084 ACGGTTTTCG
* *
1861094 AAAATATATATTTTATATAGTTTTGAAAATA-ATTTTT
1 AAAA-ATATATATTATATAGTTTTGAAAAAACATTTTT
1861131 AAAAATATATATTATATAGTTTTGAAAAAACATTTTT
1 AAAAATATATATTATATAGTTTTGAAAAAACATTTTT
*
1861168 GAAAA
1 AAAAA
1861173 CGTTTTGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 24 0.63
37 14 0.37
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.44
Consensus pattern (37 bp):
AAAAATATATATTATATAGTTTTGAAAAAACATTTTT
Found at i:1861262 original size:39 final size:37
Alignment explanation
Indices: 1861164--1861254 Score: 119
Period size: 39 Copynumber: 2.4 Consensus size: 37
1861154 GAAAAAACAT
* *
1861164 TTTTGAAAACGTTTTGAAAAATATATATAATATATAA
1 TTTTGAAAACATTTTCAAAAATATATATAATATATAA
* *
1861201 TTTAGAAAACATTTTCAAAAATATATATATAATATATGA
1 TTTTGAAAACATTTTC-AAAA-ATATATATAATATATAA
*
1861240 TTTTGAAAACCTTTT
1 TTTTGAAAACATTTT
1861255 TTAAAATAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 13 0.28
38 4 0.09
39 29 0.63
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (37 bp):
TTTTGAAAACATTTTCAAAAATATATATAATATATAA
Found at i:1861280 original size:6 final size:6
Alignment explanation
Indices: 1861269--1861310 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
1861259 AATAAATGTA
*
1861269 ATTTTC ATTTTC ATTTTC ATTTTAT ATATTTC ATTTTC ATTT
1 ATTTTC ATTTTC ATTTTC ATTTT-C AT-TTTC ATTTTC ATTT
1861311 ATTCATTTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 25 0.78
7 4 0.12
8 3 0.09
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTTC
Found at i:1862375 original size:13 final size:13
Alignment explanation
Indices: 1862357--1862382 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1862347 CTTTCATTCC
1862357 TTTTATTTACTTT
1 TTTTATTTACTTT
1862370 TTTTATTTACTTT
1 TTTTATTTACTTT
1862383 ATTTCGTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTATTTACTTT
Found at i:1869600 original size:2 final size:2
Alignment explanation
Indices: 1869589--1869621 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1869579 CTTAAAATAA
1869589 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1869622 TTTTTTTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1874072 original size:37 final size:37
Alignment explanation
Indices: 1874022--1874095 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
1874012 CAATTTTTTC
1874022 AGCTTGGTCAATGCGAAACTTCAGTGATAATGCTGTG
1 AGCTTGGTCAATGCGAAACTTCAGTGATAATGCTGTG
1874059 AGCTTGGTCAATGCGAAACTTCAGTGATAATGCTGTG
1 AGCTTGGTCAATGCGAAACTTCAGTGATAATGCTGTG
1874096 GACTTGCGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (37 bp):
AGCTTGGTCAATGCGAAACTTCAGTGATAATGCTGTG
Found at i:1874985 original size:19 final size:19
Alignment explanation
Indices: 1874963--1875000 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1874953 ACAAACGCCG
*
1874963 CAAAAGGTTGATATCTATA
1 CAAAAGGTTGAGATCTATA
1874982 CAAAAGGTTGAGATCTATA
1 CAAAAGGTTGAGATCTATA
1875001 ACGGCGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (19 bp):
CAAAAGGTTGAGATCTATA
Found at i:1878331 original size:41 final size:41
Alignment explanation
Indices: 1878197--1878332 Score: 113
Period size: 41 Copynumber: 3.3 Consensus size: 41
1878187 GTGAACCCTA
* *
1878197 TTGTGGCATTTTTATAAAAACGCCGCTAAAGTACTA-AACTG
1 TTGTGGCATTTGTATAAAAACGCCGCTAAAGTACTACTA-TG
* *
1878238 TTGTGGCATTTGTATAACAAACGCCACTATAAATGGAC--CTA--
1 TTGTGGCATTTGTATAA-AAACGCCGC--TAAA-GTACTACTATG
* *
1878279 TTGCGG-AGTTTGTATAAAAACGCCGCTGAAGTACTACTATG
1 TTGTGGCA-TTTGTATAAAAACGCCGCTAAAGTACTACTATG
*
1878320 TTGTGGCGTTTGT
1 TTGTGGCATTTGT
1878333 TGAAAAAACG
Statistics
Matches: 74, Mismatches: 10, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
37 3 0.04
38 3 0.04
39 3 0.04
40 9 0.12
41 40 0.54
42 8 0.11
44 5 0.07
45 3 0.04
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (41 bp):
TTGTGGCATTTGTATAAAAACGCCGCTAAAGTACTACTATG
Found at i:1878387 original size:82 final size:82
Alignment explanation
Indices: 1878193--1878380 Score: 236
Period size: 82 Copynumber: 2.3 Consensus size: 82
1878183 GCCAGTGAAC
* * * *
1878193 CCTATTGTGGCATTTTTATAAAAACGCCGCTAAAGTACTAAACTGTTGTGGCATTTGTATAACAA
1 CCTATTGCGGCGTTTATATAAAAACGCCGCTAAAGTACTAAACTGTTGTGGCATTTGTATAAAAA
*
1878258 ACGCCACTATAAATGGA
66 ACGCCACTACAAATGGA
* * * * *
1878275 CCTATTGCGGAGTTTGTATAAAAACGCCGCTGAAGTACTACTA-TGTTGTGGCGTTTGT-TGAAA
1 CCTATTGCGGCGTTTATATAAAAACGCCGCTAAAGTACTA-AACTGTTGTGGCATTTGTAT-AAA
* *
1878338 AAACGCCACTACATATGTA
64 AAACGCCACTACAAATGGA
1878357 CCTATTGCGGCGTTTATATAAAAA
1 CCTATTGCGGCGTTTATATAAAAA
1878381 TACCGCTACA
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
81 1 0.01
82 89 0.98
83 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (82 bp):
CCTATTGCGGCGTTTATATAAAAACGCCGCTAAAGTACTAAACTGTTGTGGCATTTGTATAAAAA
ACGCCACTACAAATGGA
Found at i:1878410 original size:82 final size:82
Alignment explanation
Indices: 1878256--1878434 Score: 191
Period size: 82 Copynumber: 2.2 Consensus size: 82
1878246 TTTGTATAAC
* * * * *
1878256 AAACGCCACTATAAATGGACCTATTGCGGAGTTTGTATAAAAACGCCGCTGAAGTACTACTATGT
1 AAACGCCACTACAAATGGACCTATTGCGGAGTTTATATAAAAACACCGCTGAAATACTACTATAT
* *
1878321 TGTGGCGTTTGTTGAAA
66 AGCGGCGTTTGTTGAAA
* * * * * *
1878338 AAACGCCACTACATATGTACCTATTGCGGCGTTTATATAAAAATACCGCT-ACAATATTACTCTA
1 AAACGCCACTACAAATGGACCTATTGCGGAGTTTATATAAAAACACCGCTGA-AATACTACTATA
* *
1878402 TAGCGGCGTTTGTTTAAG
65 TAGCGGCGTTTGTTGAAA
*
1878420 AAACGCCGCTA-AAAT
1 AAACGCCACTACAAAT
1878435 ATCATTTTGT
Statistics
Matches: 79, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
81 4 0.05
82 75 0.95
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (82 bp):
AAACGCCACTACAAATGGACCTATTGCGGAGTTTATATAAAAACACCGCTGAAATACTACTATAT
AGCGGCGTTTGTTGAAA
Found at i:1878436 original size:42 final size:41
Alignment explanation
Indices: 1878246--1878436 Score: 104
Period size: 41 Copynumber: 4.6 Consensus size: 41
1878236 TGTTGTGGCA
* * * * * *
1878246 TTTGTATAACAAACGCCACTATAA-ATGGACCTATTGCGGAG
1 TTTGTTTAA-AAACGCCGCTAAAATATGTACCTATAGCGGCG
* * * * * *
1878287 TTTGTATAAAAACGCCGCTGAAGTA-CTA-CTATGTTGTGGCG
1 TTTGTTTAAAAACGCCGCTAAAATATGTACCTA--TAGCGGCG
* * * *
1878328 TTTGTTGAAAAAACGCCACT-ACATATGTACCTATTGCGGCG
1 TTTGTT-TAAAAACGCCGCTAAAATATGTACCTATAGCGGCG
* * ** *
1878369 TTTATATAAAAATACCGCTACAATAT-TACTCTATAGCGGCG
1 TTTGTTTAAAAACGCCGCTAAAATATGTAC-CTATAGCGGCG
1878410 TTTGTTTAAGAAACGCCGCTAAAATAT
1 TTTGTTTAA-AAACGCCGCTAAAATAT
1878437 CATTTTGTGG
Statistics
Matches: 112, Mismatches: 29, Indels: 17
0.71 0.18 0.11
Matches are distributed among these distances:
39 3 0.03
40 23 0.21
41 56 0.50
42 27 0.24
43 3 0.03
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (41 bp):
TTTGTTTAAAAACGCCGCTAAAATATGTACCTATAGCGGCG
Found at i:1883286 original size:37 final size:37
Alignment explanation
Indices: 1883213--1883287 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
1883203 GTTGGAAAAT
* *
1883213 ATTTATATATTTTCTTTAAAAAATTTAAATTAATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATAATAAA
* *
1883250 ATTTATATAATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTAAAAATAATAAA
1883287 A
1 A
1883288 AGATTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATAATAAA
Found at i:1887819 original size:22 final size:22
Alignment explanation
Indices: 1887794--1887844 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1887784 CTACGGCGAC
*
1887794 ATCCGTTCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
1887816 ATCCGTCCCCGTCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
1887838 ATCCGTC
1 ATCCGTC
1887845 TATCTCCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.18, C:0.43, G:0.18, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:1888262 original size:14 final size:14
Alignment explanation
Indices: 1888245--1888276 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1888235 GCGATTTTAG
1888245 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
*
1888259 TTTCTCGTTGCGAT
1 TTTCGCGTTGCGAT
1888273 TTTC
1 TTTC
1888277 ATTTCGCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.22, G:0.22, T:0.50
Consensus pattern (14 bp):
TTTCGCGTTGCGAT
Found at i:1888282 original size:33 final size:34
Alignment explanation
Indices: 1888235--1888368 Score: 110
Period size: 33 Copynumber: 3.8 Consensus size: 34
1888225 AAATCGCAAC
1888235 GCGATTTT-AGTTTCGCGTTGCGATTTTCTCGTT
1 GCGATTTTCAGTTTCGCGTTGCGATTTTCTCGTT
* * *
1888268 GCGATTTTCA-TTTCGCGTTGTGATTATCTCATT
1 GCGATTTTCAGTTTCGCGTTGCGATTTTCTCGTT
** ** *
1888301 GCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTT
1 GCGATTTTCAGTTTCGCGTTGCGAT--T--TTCTC--GTT
* *
1888341 GCGATTTTCATTTTCGTGTTGCGATTTT
1 GCGATTTTCAGTTTCGCGTTGCGATTTT
1888369 AAGTTTCAGA
Statistics
Matches: 78, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
33 36 0.46
34 13 0.17
36 3 0.04
38 4 0.05
40 22 0.28
ACGTcount: A:0.14, C:0.17, G:0.22, T:0.46
Consensus pattern (34 bp):
GCGATTTTCAGTTTCGCGTTGCGATTTTCTCGTT
Found at i:1888324 original size:20 final size:20
Alignment explanation
Indices: 1888299--1888345 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1888289 GATTATCTCA
1888299 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
** *
1888319 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCAAATTCGCG
1888339 TTGCGAT
1 TTGCGAT
1888346 TTTCATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:1888351 original size:20 final size:20
Alignment explanation
Indices: 1888313--1888368 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1888303 GATAGTCAAA
* **
1888313 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
1888333 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
1888353 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
1888369 AAGTTTCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:1888375 original size:20 final size:20
Alignment explanation
Indices: 1888332--1888375 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1888322 CGATAGTCAT
* *
1888332 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
1888352 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
1888372 TTTC
1 TTTC
1888376 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:1890303 original size:20 final size:20
Alignment explanation
Indices: 1890278--1890346 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
1890268 CGAAACTAAA
1890278 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1890298 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
1890318 ATCGCAACGTGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
1890338 ATCACAACG
1 ATCGCAACG
1890347 GGATAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1890445 original size:19 final size:20
Alignment explanation
Indices: 1890418--1890456 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1890408 GCAACGCGAA
* *
1890418 TTTAGTTTCTCGTTGCGATT
1 TTTAGTTTCGCATTGCGATT
1890438 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCGCATTGCGATT
1890457 ATCTTGTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.13, C:0.15, G:0.18, T:0.54
Consensus pattern (20 bp):
TTTAGTTTCGCATTGCGATT
Found at i:1890487 original size:20 final size:20
Alignment explanation
Indices: 1890462--1890509 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1890452 CGATTATCTT
1890462 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
**
1890482 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAAATTCGC
1890502 GTTGCGAT
1 GTTGCGAT
1890510 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGC
Found at i:1890519 original size:20 final size:20
Alignment explanation
Indices: 1890477--1890539 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
1890467 GATAGTCAAA
** * *
1890477 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATTTTAAGT
1890497 TTCGCGTTGCGATTTTAAGT
1 TTCGCGTTGCGATTTTAAGT
*
1890517 TTCGTGTTGCGATTTTAAGT
1 TTCGCGTTGCGATTTTAAGT
1890537 TTC
1 TTC
1890540 AGAAACTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.14, C:0.16, G:0.24, T:0.46
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTAAGT
Found at i:1891047 original size:21 final size:21
Alignment explanation
Indices: 1891021--1891098 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
1891011 CTCACCTGTC
1891021 ATCGTTCAAGAGGCCTCTCCT
1 ATCGTTCAAGAGGCCTCTCCT
* **
1891042 ATCGTTCAAGAGGCCCCTATT
1 ATCGTTCAAGAGGCCTCTCCT
** * *
1891063 ATCCCTCAAGAGTCCTCTCCC
1 ATCGTTCAAGAGGCCTCTCCT
1891084 ATCGTTCAAGAGGCC
1 ATCGTTCAAGAGGCC
1891099 CTTCCCACCA
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.26
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCTCTCCT
Found at i:1891104 original size:21 final size:22
Alignment explanation
Indices: 1891020--1891116 Score: 85
Period size: 21 Copynumber: 4.6 Consensus size: 22
1891010 ACTCACCTGT
1891020 CATCGTTCAAGAGG-CCTCTCC
1 CATCGTTCAAGAGGCCCTCTCC
* **
1891041 TATCGTTCAAGAGGCCC-CTAT
1 CATCGTTCAAGAGGCCCTCTCC
* ** *
1891062 TATCCCTCAAGA-GTCCTCTCC
1 CATCGTTCAAGAGGCCCTCTCC
1891083 CATCGTTCAAGAGGCCCT-TCC
1 CATCGTTCAAGAGGCCCTCTCC
* *
1891104 CACCATTCAAGAG
1 CATCGTTCAAGAG
1891117 CCCGATTCAC
Statistics
Matches: 59, Mismatches: 14, Indels: 6
0.75 0.18 0.08
Matches are distributed among these distances:
20 3 0.05
21 50 0.85
22 6 0.10
ACGTcount: A:0.23, C:0.36, G:0.16, T:0.25
Consensus pattern (22 bp):
CATCGTTCAAGAGGCCCTCTCC
Found at i:1891114 original size:42 final size:42
Alignment explanation
Indices: 1891020--1891116 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
1891010 ACTCACCTGT
* * *
1891020 CATCGTTCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCCTAT
1 CATCCTTCAAGAGGCCTCTCCCATCGTTCAAGAGGCCCCTAC
* * * * *
1891062 TATCCCTCAAGAGTCCTCTCCCATCGTTCAAGAGGCCCTTCC
1 CATCCTTCAAGAGGCCTCTCCCATCGTTCAAGAGGCCCCTAC
1891104 CA-CCATTCAAGAG
1 CATCC-TTCAAGAG
1891117 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
41 2 0.05
42 42 0.95
ACGTcount: A:0.23, C:0.36, G:0.16, T:0.25
Consensus pattern (42 bp):
CATCCTTCAAGAGGCCTCTCCCATCGTTCAAGAGGCCCCTAC
Found at i:1892522 original size:14 final size:14
Alignment explanation
Indices: 1892503--1892539 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1892493 GCTTGTTTAA
1892503 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
1892517 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
1892531 TTGATTTGT
1 TTGATTTGT
1892540 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1892706 original size:20 final size:20
Alignment explanation
Indices: 1892681--1892736 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1892671 ACTCGAAATT
1892681 GCAATGCGAAAGTCAAAAGC
1 GCAATGCGAAAGTCAAAAGC
* *
1892701 GCAATGCGAAAGCCAAAATC
1 GCAATGCGAAAGTCAAAAGC
*
1892721 GCAACGCGAAAGTCAA
1 GCAATGCGAAAGTCAA
1892737 TTCGCGTTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.09
Consensus pattern (20 bp):
GCAATGCGAAAGTCAAAAGC
Found at i:1892805 original size:34 final size:33
Alignment explanation
Indices: 1892741--1892871 Score: 147
Period size: 34 Copynumber: 3.9 Consensus size: 33
1892731 AGTCAATTCG
* ** *
1892741 CGTTGCGATAGTCTAATAT-GTTTTGTGATTTTCT
1 CGTTGCGATAGTCAAAT-TCGCGTTGCGATTTT-T
*
1892775 CGTTGCGATAGTCAAATTCACGTTGCGATTTTTT
1 CGTTGCGATAGTCAAATTCGCGTTGCGA-TTTTT
* * *
1892809 TGTTGCGATAGTAAAATTCGCTTTGCGATTTTT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
1892842 GCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 -CGTTGCGATAGTCAAATTCGCGTTGCGAT
1892872 ATTCAAATGA
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
33 6 0.07
34 72 0.88
35 4 0.05
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (33 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
Found at i:1892867 original size:20 final size:20
Alignment explanation
Indices: 1892842--1892879 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1892832 TGCGATTTTT
1892842 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
*
1892862 GCGTTGCGATATTCAAAT
1 GCGTTGCGATAGTCAAAT
1892880 GAATGTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:1893102 original size:140 final size:140
Alignment explanation
Indices: 1892850--1893132 Score: 521
Period size: 140 Copynumber: 2.0 Consensus size: 140
1892840 TTGCGTTGCG
*
1892850 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAGCTAAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTAAACAGATCA
*
1892915 TAGCAATGTTCAAACTCAAGTTACTAATACATGTCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1892980 AATACAAATA
131 AATACAAATA
* *
1892990 ATAGTCAAATTCGCGTTGCGATTTTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTAAACAGATCA
1893055 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
*
1893120 AATACACATA
131 AATACAAATA
1893130 ATA
1 ATA
1893133 CAACATTTGC
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 138 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTAAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACAAATA
Found at i:1893196 original size:6 final size:6
Alignment explanation
Indices: 1893185--1893225 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
1893175 AGGTGAAGCC
* * *
1893185 GATTGT GATTGT GATTTT GATTTT GATTGT GATTTT GATTG
1 GATTGT GATTGT GATTGT GATTGT GATTGT GATTGT GATTG
1893226 CCTTTTTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.56
Consensus pattern (6 bp):
GATTGT
Found at i:1893200 original size:12 final size:12
Alignment explanation
Indices: 1893185--1893225 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
1893175 AGGTGAAGCC
*
1893185 GATTGTGATTGT
1 GATTGTGATTTT
*
1893197 GATTTTGATTTT
1 GATTGTGATTTT
1893209 GATTGTGATTTT
1 GATTGTGATTTT
1893221 GATTG
1 GATTG
1893226 CCTTTTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.56
Consensus pattern (12 bp):
GATTGTGATTTT
Found at i:1893206 original size:18 final size:18
Alignment explanation
Indices: 1893185--1893225 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1893175 AGGTGAAGCC
1893185 GATTGTGATTGTGATTTT
1 GATTGTGATTGTGATTTT
*
1893203 GATTTTGATTGTGATTTT
1 GATTGTGATTGTGATTTT
1893221 GATTG
1 GATTG
1893226 CCTTTTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.56
Consensus pattern (18 bp):
GATTGTGATTGTGATTTT
Found at i:1895295 original size:15 final size:14
Alignment explanation
Indices: 1895259--1895295 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1895249 TCCCATGGCA
1895259 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
1895273 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
1895287 TTATTCTTC
1 TT-TTCTTC
1895296 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.08, C:0.19, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:1896397 original size:19 final size:19
Alignment explanation
Indices: 1896373--1896411 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1896363 TATGTATTAT
1896373 TGCGTTGCGATAGACAGAA
1 TGCGTTGCGATAGACAGAA
*
1896392 TGCGTTGCGATAGTCAGAA
1 TGCGTTGCGATAGACAGAA
1896411 T
1 T
1896412 CGTGTTGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (19 bp):
TGCGTTGCGATAGACAGAA
Found at i:1897343 original size:29 final size:29
Alignment explanation
Indices: 1897281--1897349 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
1897271 ACCGTTGGTC
**
1897281 GGGTGCTATTTTGGGAATTTATTCGAAAT
1 GGGTGCTATTTTGGGAATTTATTAAAAAT
* *
1897310 GGGTGCTATTTTGGTAATTATTTTAAAAAT
1 GGGTGCTATTTTGGGAATT-TATTAAAAAT
*
1897340 -GGTGTTATTT
1 GGGTGCTATTT
1897350 CTGTAAAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 27 0.79
30 7 0.21
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.46
Consensus pattern (29 bp):
GGGTGCTATTTTGGGAATTTATTAAAAAT
Found at i:1899213 original size:10 final size:10
Alignment explanation
Indices: 1899185--1899220 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1899175 TCGCCAATTA
**
1899185 TTTTTTTTCT
1 TTTTTTTTAG
1899195 TTTTTTTTAG
1 TTTTTTTTAG
1899205 TTTTTTTTAG
1 TTTTTTTTAG
1899215 TTTTTT
1 TTTTTT
1899221 AATGATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.86
Consensus pattern (10 bp):
TTTTTTTTAG
Found at i:1899286 original size:23 final size:23
Alignment explanation
Indices: 1899260--1899310 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1899250 TTTATTTATA
*
1899260 TCTTTATGACTCATTTATCTCTG
1 TCTTTATGACACATTTATCTCTG
* * * *
1899283 TCTTTGTGGCACGTTTTTCTCTG
1 TCTTTATGACACATTTATCTCTG
1899306 TCTTT
1 TCTTT
1899311 TGGTAGTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.10, C:0.22, G:0.14, T:0.55
Consensus pattern (23 bp):
TCTTTATGACACATTTATCTCTG
Found at i:1900008 original size:19 final size:19
Alignment explanation
Indices: 1899980--1900167 Score: 89
Period size: 21 Copynumber: 9.6 Consensus size: 19
1899970 TCCAAGTTCG
1899980 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
*
1899999 CGTTGTGATTTTCCAAA-T
1 CGTTGCGATTTTCCAAATT
* *
1900017 --TTACG-TTAGTCCAAATT
1 CGTTGCGATT-TTCCAAATT
* *
1900034 CGTTGCGATAGTT-CAAGTT
1 CGTTGCGAT-TTTCCAAATT
*
1900053 CACGTTGTGATTTTCCAAATT
1 --CGTTGCGATTTTCCAAATT
* ** * *
1900074 CATTGCGATAGTCGAAGTT
1 CGTTGCGATTTTCCAAATT
** * *
1900093 CGCGTTGCGATAGTCGAAGTT
1 --CGTTGCGATTTTCCAAATT
1900114 CGCATTGCGATTTTCCAAATT
1 CG--TTGCGATTTTCCAAATT
** *
1900135 CGTTGCGATAGTCCAAGTT
1 CGTTGCGATTTTCCAAATT
1900154 CGCGTTGCGATTTT
1 --CGTTGCGATTTT
1900168 GGAAAATCGC
Statistics
Matches: 127, Mismatches: 27, Indels: 28
0.70 0.15 0.15
Matches are distributed among these distances:
15 2 0.02
16 9 0.07
17 1 0.01
18 1 0.01
19 54 0.43
20 4 0.03
21 56 0.44
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:1900058 original size:35 final size:35
Alignment explanation
Indices: 1899991--1900058 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
1899981 GTTGCGATTT
* * *
1899991 TCCAAATTCGTTGTGATTTTCCAAATTTACGTTAG
1 TCCAAATTCGTTGCGATGTTCCAAATTCACGTTAG
*
1900026 TCCAAATTCGTTGCGATAGTT-CAAGTTCACGTT
1 TCCAAATTCGTTGCGAT-GTTCCAAATTCACGTT
1900059 GTGATTTTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 26 0.93
36 2 0.07
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (35 bp):
TCCAAATTCGTTGCGATGTTCCAAATTCACGTTAG
Found at i:1900126 original size:61 final size:58
Alignment explanation
Indices: 1899961--1900164 Score: 229
Period size: 61 Copynumber: 3.5 Consensus size: 58
1899951 CAACGCGATT
** *
1899961 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG-TTGTGATTTTCCAAA-T-
1 TTGCGATAGTCCAAGTTCGCGTTGCGATAGT-CAAGTTCGCTTGTGATTTTCCAAATTC
* * * *
1900017 TTACGTTAGTCCAAATT--CGTTGCGATAGTTCAAGTTCACGTTGTGATTTTCCAAATTC
1 TTGCGATAGTCCAAGTTCGCGTTGCGATAG-TCAAGTTCGC-TTGTGATTTTCCAAATTC
* *
1900075 ATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCATTGCGATTTTCCAAATTC
1 -TTGCGATAGTCCAAGTTCGCGTTGCGATAGTC-AAGTTCGC-TTGTGATTTTCCAAATTC
1900136 GTTGCGATAGTCCAAGTTCGCGTTGCGAT
1 -TTGCGATAGTCCAAGTTCGCGTTGCGAT
1900165 TTTGGAAAAT
Statistics
Matches: 123, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
54 15 0.12
55 1 0.01
56 29 0.24
57 1 0.01
59 13 0.11
60 2 0.02
61 62 0.50
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (58 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCAAGTTCGCTTGTGATTTTCCAAATTC
Found at i:1900591 original size:19 final size:19
Alignment explanation
Indices: 1900567--1900675 Score: 101
Period size: 19 Copynumber: 5.4 Consensus size: 19
1900557 TTATTTTGGT
*
1900567 TTTTTCACTATCGCAGCAC
1 TTTTTCACTATCGCAACAC
1900586 TTTTTCACTATCGCAACAACAC
1 TTTTTCACTATCG---CAACAC
*
1900608 GTTTTTCAAACTCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* *
1900630 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
* *
1900649 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
1900668 ATTTTTCA
1 -TTTTTCA
1900676 AAATCGTTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
19 44 0.58
20 5 0.07
21 4 0.05
22 11 0.14
23 6 0.08
25 6 0.08
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.35
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:1901752 original size:58 final size:58
Alignment explanation
Indices: 1901623--1901752 Score: 156
Period size: 58 Copynumber: 2.2 Consensus size: 58
1901613 TCAAGTGATT
* *
1901623 ATTTTGTAGCTTTTAATGGTTGAGAGACTCAACAAAGCATTATATATAATCGAGAGATC
1 ATTTTGTA-CTTTTAATAGTTAAGAGACTCAACAAAGCATTATATATAATCGAGAGATC
* * * *
1901682 ATTTTGTAACTTTTAATAGTTAAG-GACTCAACAAATCATTATCATATAGT-TAGGGATC
1 ATTTTGT-ACTTTTAATAGTTAAGAGACTCAACAAAGCATTAT-ATATAATCGAGAGATC
1901740 ATTTGTGTACTTT
1 ATTT-TGTACTTT
1901753 CCTATTAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
58 32 0.52
59 29 0.47
60 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (58 bp):
ATTTTGTACTTTTAATAGTTAAGAGACTCAACAAAGCATTATATATAATCGAGAGATC
Found at i:1902864 original size:20 final size:20
Alignment explanation
Indices: 1902817--1902857 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1902807 TTATGGTAGG
1902817 AGATGAATTTTTAAAATTTT
1 AGATGAATTTTTAAAATTTT
1902837 AGATGAATTTTTAAAATTTT
1 AGATGAATTTTTAAAATTTT
1902857 A
1 A
1902858 ATGGAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (20 bp):
AGATGAATTTTTAAAATTTT
Found at i:1903566 original size:23 final size:22
Alignment explanation
Indices: 1903540--1903583 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1903530 TAATTTTTAA
1903540 ATAGGGAGGTACCAATACCCCTC
1 ATAGGG-GGTACCAATACCCCTC
* *
1903563 ATAGGGTGTACCGATACCCCT
1 ATAGGGGGTACCAATACCCCT
1903584 ATGCCAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (22 bp):
ATAGGGGGTACCAATACCCCTC
Found at i:1903685 original size:74 final size:74
Alignment explanation
Indices: 1903570--1903732 Score: 229
Period size: 74 Copynumber: 2.2 Consensus size: 74
1903560 CTCATAGGGT
* *
1903570 GTACCGATACCCCTATGCCAAATTTTGGCTCCGAGAAAAACATATTGCCCAATGGATACCGATAC
1 GTACCGATACCCCTATGCCAAATTTTGGCTCCGAGAAAAACAGAATGCCCAATGGATACCGATAC
1903635 CCCATATAGG
66 CCCATAT-GG
** * * * *
1903645 GTACCGATACCCCTATG-CATGTTTTGGGTCCGAGAGAAACAGAATGCCCTATGGGTACCGATAC
1 GTACCGATACCCCTATGCCAAATTTTGGCTCCGAGAAAAACAGAATGCCCAATGGATACCGATAC
*
1903709 CCCTTATGG
66 CCCATATGG
1903718 GTACCGATACCCCTA
1 GTACCGATACCCCTA
1903733 GTCATTTAAC
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
73 17 0.22
74 45 0.57
75 17 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (74 bp):
GTACCGATACCCCTATGCCAAATTTTGGCTCCGAGAAAAACAGAATGCCCAATGGATACCGATAC
CCCATATGG
Found at i:1903718 original size:19 final size:19
Alignment explanation
Indices: 1903694--1903731 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1903684 CAGAATGCCC
1903694 TATGGGTACCGATACCCCT
1 TATGGGTACCGATACCCCT
1903713 TATGGGTACCGATACCCCT
1 TATGGGTACCGATACCCCT
1903732 AGTCATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.26
Consensus pattern (19 bp):
TATGGGTACCGATACCCCT
Found at i:1911442 original size:23 final size:22
Alignment explanation
Indices: 1911416--1911459 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1911406 TAATTTTTAA
1911416 ATAGGGAGGTACCAATACCCCTC
1 ATAGGG-GGTACCAATACCCCTC
* *
1911439 ATAGGGTGTACCGATACCCCT
1 ATAGGGGGTACCAATACCCCT
1911460 ATGCCAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (22 bp):
ATAGGGGGTACCAATACCCCTC
Found at i:1914303 original size:10 final size:11
Alignment explanation
Indices: 1914276--1914303 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1914266 CAATAAAAAT
1914276 ATAAAAACAAC
1 ATAAAAACAAC
1914287 ATAAAAACAAC
1 ATAAAAACAAC
1914298 ATAAAA
1 ATAAAA
1914304 TAAAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.75, C:0.14, G:0.00, T:0.11
Consensus pattern (11 bp):
ATAAAAACAAC
Found at i:1914776 original size:109 final size:110
Alignment explanation
Indices: 1914564--1914777 Score: 261
Period size: 109 Copynumber: 2.0 Consensus size: 110
1914554 GGGGGACCTA
* * * *
1914564 GAATGATATTTTACCAAAAAAGTACAAAGCATACATGTGAATGGGAAAATTATGAAAATAATCCC
1 GAATGATATTTTACCAAAAAAGCACAAAGCATACATATAAATGGGAAAATTATGAAAAAAATCCC
* ** * ** *
1914629 TAACAGTGAGTATTTTGCAAAAATATGACAAAGTTTGGGGATTTG
66 TAACAATGACCATTTTGCAAAAACACAACAAAGCTTGGGGATTTG
* *
1914674 GAATGATATTTTACCAAAAAA-CAGAAAGCATACATATAAATTGGAAAATTAT-AAAAAAAGTCC
1 GAATGATATTTTACCAAAAAAGCACAAAGCATACATATAAATGGGAAAATTATGAAAAAAA-TCC
* * *
1914737 CTGACAATGACCATTTTGTAAAAACACAAGAAAGCTTGGGG
65 CTAACAATGACCATTTTGCAAAAACACAACAAAGCTTGGGG
1914778 GACTTAAAAC
Statistics
Matches: 87, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
108 6 0.07
109 60 0.69
110 21 0.24
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (110 bp):
GAATGATATTTTACCAAAAAAGCACAAAGCATACATATAAATGGGAAAATTATGAAAAAAATCCC
TAACAATGACCATTTTGCAAAAACACAACAAAGCTTGGGGATTTG
Found at i:1915721 original size:111 final size:111
Alignment explanation
Indices: 1915577--1915777 Score: 332
Period size: 111 Copynumber: 1.8 Consensus size: 111
1915567 CGTGTATTTA
* *
1915577 CAAAATGATCACTGTCAGGGACCATTTTTATAATTTTCCAATTTACATGTATGCTTTGTATTTTT
1 CAAAATGATCACTGTCAGGGACCATTTTCATAATTTTCCAATTCACATGTATGCTTTGTATTTTT
1915642 TGGTAAAATATCATTCCAGGTCCCCAAACTTTTCCTTACTTTTTTG
66 TGGTAAAATATCATTCCAGGTCCCCAAACTTTTCCTTACTTTTTTG
* * * *
1915688 CAAAAT-ATTCACTGTGAGTGACGATTTTCATAATTTTCCCATTCACATGTATGCTTTGTATTTT
1 CAAAATGA-TCACTGTCAGGGACCATTTTCATAATTTTCCAATTCACATGTATGCTTTGTATTTT
1915752 TTGGTAAAATATCATTCCAGGTCCCC
65 TTGGTAAAATATCATTCCAGGTCCCC
1915778 CTATGTTTGT
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
110 1 0.01
111 82 0.99
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.42
Consensus pattern (111 bp):
CAAAATGATCACTGTCAGGGACCATTTTCATAATTTTCCAATTCACATGTATGCTTTGTATTTTT
TGGTAAAATATCATTCCAGGTCCCCAAACTTTTCCTTACTTTTTTG
Found at i:1915900 original size:22 final size:21
Alignment explanation
Indices: 1915857--1915910 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
1915847 CTGTTTTGTT
1915857 TTATTT-TAATTTAGTCACTA
1 TTATTTCTAATTTAGTCACTA
*
1915877 TTAATTTCTAATTTAG-CTATTA
1 TT-ATTTCTAATTTAGTC-ACTA
1915899 TTA-TTCTAATTT
1 TTATTTCTAATTT
1915911 TTGCATTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 11 0.37
21 6 0.20
22 13 0.43
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (21 bp):
TTATTTCTAATTTAGTCACTA
Found at i:1916041 original size:33 final size:31
Alignment explanation
Indices: 1916004--1916089 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 31
1915994 CAATTAGGTC
*
1916004 CTTGTACTTATGTTTATTCTATTTTTATTTTAT
1 CTTGTA-TTATATTTATT-TATTTTTATTTTAT
*
1916037 CTTGT-TTTTATTTATTTA--TTTATTTTAT
1 CTTGTATTATATTTATTTATTTTTATTTTAT
* * *
1916065 TTTTTATTATTTTTATTTTATTTTT
1 CTTGTATTATATTTA-TTTATTTTT
1916090 TTAAATTAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
28 13 0.30
29 7 0.16
30 6 0.14
31 9 0.21
32 3 0.07
33 5 0.12
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.74
Consensus pattern (31 bp):
CTTGTATTATATTTATTTATTTTTATTTTAT
Found at i:1916044 original size:16 final size:16
Alignment explanation
Indices: 1916023--1916085 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
1916013 ATGTTTATTC
*
1916023 TATTTTTATTTTATCT
1 TATTTTTATTTTATAT
* *
1916039 TGTTTTTATTTATTTAT
1 TATTTTTATTT-TATAT
*
1916056 T-TATTTTATTTTTTAT
1 TAT-TTTTATTTTATAT
1916072 TATTTTTATTTTAT
1 TATTTTTATTTTAT
1916086 TTTTTTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
16 27 0.68
17 13 0.32
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.78
Consensus pattern (16 bp):
TATTTTTATTTTATAT
Found at i:1916081 original size:21 final size:24
Alignment explanation
Indices: 1916041--1916090 Score: 79
Period size: 21 Copynumber: 2.2 Consensus size: 24
1916031 TTTTATCTTG
1916041 TTTTTATTTATTTATTTATTTTAT
1 TTTTTATTTATTTATTTATTTTAT
1916065 TTTTTA-TTA-TT-TTTATTTTAT
1 TTTTTATTTATTTATTTATTTTAT
1916086 TTTTT
1 TTTTT
1916091 TAAATTAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.58
22 2 0.08
23 3 0.12
24 6 0.23
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (24 bp):
TTTTTATTTATTTATTTATTTTAT
Found at i:1916085 original size:11 final size:11
Alignment explanation
Indices: 1916011--1916089 Score: 64
Period size: 11 Copynumber: 7.7 Consensus size: 11
1916001 GTCCTTGTAC
*
1916011 TTATGTTTATT
1 TTATTTTTATT
*
1916022 CTATTTTTATT
1 TTATTTTTATT
*
1916033 TTATCTTGT-TT
1 TTAT-TTTTATT
1916044 TTA--TTTA-T
1 TTATTTTTATT
1916052 TTA--TTTATT
1 TTATTTTTATT
*
1916061 TTATTTTT-TA
1 TTATTTTTATT
1916071 TTATTTTTATT
1 TTATTTTTATT
1916082 TTATTTTT
1 TTATTTTT
1916090 TTAAATTAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
8 10 0.18
9 4 0.07
10 9 0.16
11 29 0.53
12 3 0.05
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.77
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:1917467 original size:3 final size:3
Alignment explanation
Indices: 1917454--1917502 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
1917444 CTTAAACAAA
* *
1917454 TAT TA- TAT TAT TA- TATT TAT TAT TAT TAA TAT TAT TAG TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
1917498 TAT TA
1 TAT TA
1917503 ATAATAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.85
4 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1923856 original size:2 final size:2
Alignment explanation
Indices: 1923844--1923893 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1923834 TCATTTATCC
*
1923844 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1923886 AT AT AT AT
1 AT AT AT AT
1923894 CCCTAGTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1924139 original size:22 final size:22
Alignment explanation
Indices: 1924090--1924152 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
1924080 CAAAGAGCAA
* *
1924090 AAAGAAAAGGAAAAAAGAAATT
1 AAAGCAAAGAAAAAAAGAAATT
1924112 AAAGCAAAGAAAAAATAGAAA-T
1 AAAGCAAAGAAAAAA-AGAAATT
* *
1924134 AGAGCAAA-AAGAAAAGAAA
1 AAAGCAAAGAAAAAAAGAAA
1924153 AAGAAATAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.14
21 5 0.14
22 21 0.58
23 5 0.14
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.06
Consensus pattern (22 bp):
AAAGCAAAGAAAAAAAGAAATT
Found at i:1924143 original size:38 final size:34
Alignment explanation
Indices: 1924101--1924195 Score: 113
Period size: 32 Copynumber: 2.7 Consensus size: 34
1924091 AAGAAAAGGA
1924101 AAAAAGAAATTAAAGCAAAGAAAAAATAGAAATAGAGC
1 AAAAAGAAA--AAAG-AAA-AAAAAATAGAAATAGAGC
*
1924139 AAAAAG--AAAAGAAAAAGAAATAGAAATAGAGC
1 AAAAAGAAAAAAGAAAAAAAAATAGAAATAGAGC
1924171 AAAAAGAAAAGAAGAAGAAAAAAAT
1 AAAAAGAAAA-AAGAA-AAAAAAAT
1924196 TAAAGAAAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
32 23 0.45
33 3 0.06
34 6 0.12
35 5 0.10
36 8 0.16
38 6 0.12
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.07
Consensus pattern (34 bp):
AAAAAGAAAAAAGAAAAAAAAATAGAAATAGAGC
Found at i:1924155 original size:11 final size:11
Alignment explanation
Indices: 1924139--1924214 Score: 68
Period size: 11 Copynumber: 6.8 Consensus size: 11
1924129 GAAATAGAGC
1924139 AAAAAGAAAAG
1 AAAAAGAAAAG
1924150 AAAAAGAAATAG
1 AAAAAGAAA-AG
*
1924162 AAATAG---AG
1 AAAAAGAAAAG
1924170 CAAAAAGAAAAG
1 -AAAAAGAAAAG
* *
1924182 AAGAAGAAAAA
1 AAAAAGAAAAG
1924193 AATTAAAGAAAAG
1 AA--AAAGAAAAG
1924206 AAAAAGAAA
1 AAAAAGAAA
1924215 CAAATAGCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
8 2 0.04
9 5 0.10
11 27 0.52
12 9 0.17
13 9 0.17
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.05
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:1924165 original size:32 final size:32
Alignment explanation
Indices: 1924124--1924190 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
1924114 AGCAAAGAAA
1924124 AAATAGAAATAGAGCAAAAAGAAAAGAAAAAG
1 AAATAGAAATAGAGCAAAAAGAAAAGAAAAAG
*
1924156 AAATAGAAATAGAGCAAAAAGAAAAGAAGAAG
1 AAATAGAAATAGAGCAAAAAGAAAAGAAAAAG
1924188 AAA
1 AAA
1924191 AAAATTAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.72, C:0.03, G:0.19, T:0.06
Consensus pattern (32 bp):
AAATAGAAATAGAGCAAAAAGAAAAGAAAAAG
Found at i:1924180 original size:6 final size:6
Alignment explanation
Indices: 1924139--1924214 Score: 61
Period size: 6 Copynumber: 12.5 Consensus size: 6
1924129 GAAATAGAGC
* *
1924139 AAAAAG -AAAAG AAAAAG AAATAG AAATAGAG CAAAAAG -AAAAG AAGAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA-A-AG -AAAAAG AAAAAG AAAAAG
1924188 AAAAA- AATTAAAG -AAAAG AAAAAG AAA
1 AAAAAG AA--AAAG AAAAAG AAAAAG AAA
1924215 CAAATAGCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
5 16 0.28
6 29 0.51
7 6 0.11
8 3 0.05
9 3 0.05
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.05
Consensus pattern (6 bp):
AAAAAG
Found at i:1924205 original size:24 final size:24
Alignment explanation
Indices: 1924173--1924219 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1924163 AATAGAGCAA
*
1924173 AAAGAAAAGAAGAAGAAAAAAATT
1 AAAGAAAAGAAAAAGAAAAAAATT
*
1924197 AAAGAAAAGAAAAAGAAACAAAT
1 AAAGAAAAGAAAAAGAAAAAAAT
1924220 AGCAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (24 bp):
AAAGAAAAGAAAAAGAAAAAAATT
Found at i:1925350 original size:33 final size:32
Alignment explanation
Indices: 1925247--1925381 Score: 198
Period size: 32 Copynumber: 4.2 Consensus size: 32
1925237 AAGCAATAGA
*
1925247 GGGCATCTTTGAAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
1925279 GGGCATCTTTAGAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
1925311 GAGCATCTTTGGAGATTCAACATCAAAATGTTG
1 GGGCATCTTTGGAGATTCAACATC-AAATGTTG
* ** *
1925344 GGGCATCTTTGGAGATTCAATATTGAATATTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
1925376 GGGCAT
1 GGGCAT
1925382 TCAATATCCT
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
32 64 0.69
33 29 0.31
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (32 bp):
GGGCATCTTTGGAGATTCAACATCAAATGTTG
Found at i:1925540 original size:34 final size:34
Alignment explanation
Indices: 1925494--1925614 Score: 165
Period size: 34 Copynumber: 3.6 Consensus size: 34
1925484 AATTTTTTTT
* * * *
1925494 GTCTCACTTGAGATAATTTTTCAAAACAAATTTT
1 GTCTCGCTTGAGACAATTTCTCAAAACAAATTTC
1925528 GTCATAC-C-TGAGACAATTTCTCAAAACAAATTTC
1 GTC-T-CGCTTGAGACAATTTCTCAAAACAAATTTC
*
1925562 GTCTCGCTTGAAACAATTTCTCAAAACAAATTTC
1 GTCTCGCTTGAGACAATTTCTCAAAACAAATTTC
1925596 GTCTCGCTTGAGACAATTT
1 GTCTCGCTTGAGACAATTT
1925615 TTCTCTGAGA
Statistics
Matches: 78, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
32 1 0.01
33 2 0.03
34 72 0.92
35 2 0.03
36 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.35
Consensus pattern (34 bp):
GTCTCGCTTGAGACAATTTCTCAAAACAAATTTC
Found at i:1926085 original size:40 final size:40
Alignment explanation
Indices: 1925996--1926136 Score: 128
Period size: 40 Copynumber: 3.5 Consensus size: 40
1925986 TAAAGAATAT
* * *
1925996 TTTATCTCACTTGAGATAG-TTTCCCTCTAAACAA-AAGA
1 TTTATCTCACTTGAGACAGTTTTTCCTCGAAACAATAAGA
* *
1926034 TTTTGTCTCACTTGAGACAGTTTTTGCTCGAAACAATAAGA
1 -TTTATCTCACTTGAGACAGTTTTTCCTCGAAACAATAAGA
* ** *
1926075 TTTATTTCACTCAAGATC-GTTTTTCCTTGAAAC-ATAAGA
1 TTTATCTCACTTGAGA-CAGTTTTTCCTCGAAACAATAAGA
* *
1926114 TTTTATCTCGCTTGAGATAGTTT
1 -TTTATCTCACTTGAGACAGTTT
1926137 CCCTAGAAAT
Statistics
Matches: 81, Mismatches: 16, Indels: 9
0.76 0.15 0.08
Matches are distributed among these distances:
39 23 0.28
40 53 0.65
41 5 0.06
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (40 bp):
TTTATCTCACTTGAGACAGTTTTTCCTCGAAACAATAAGA
Found at i:1926200 original size:36 final size:36
Alignment explanation
Indices: 1926099--1926292 Score: 219
Period size: 36 Copynumber: 5.3 Consensus size: 36
1926089 GATCGTTTTT
* * *
1926099 CCTTGAAACATAAGATTTTATCTCGCTTGAGATAGTTTC
1 CCTTGAAAC--AA-ATTTTGTCTCCCTTGAGACAGTTTC
* * * *
1926138 CCTAGAAA-TAGTTTTGTCTCTCTTGAGACAGTTTC
1 CCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTC
* * * *
1926173 CCTAGAAACGAGTTTTGTCTCCTTTGAGACAGTTTC
1 CCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTC
*
1926209 CCTTGAAACAAATTTTGTCTCCCTTGAGACGGTTTC
1 CCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTC
* *
1926245 CCTTGAAACAAATTTTATCTCCCTTGAGACAATTTC
1 CCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTC
*
1926281 ACTTGAAACAAA
1 CCTTGAAACAAA
1926293 AGATTTTATC
Statistics
Matches: 136, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
35 29 0.21
36 100 0.74
39 7 0.05
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (36 bp):
CCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTC
Found at i:1926328 original size:39 final size:39
Alignment explanation
Indices: 1925994--1926338 Score: 218
Period size: 36 Copynumber: 9.1 Consensus size: 39
1925984 TTTAAAGAAT
* *
1925994 ATTTTATCTCACTTGAGATAGTTTCCCTCTAAACAAAAG
1 ATTTTATCTCACTTGAGACAGTTTCCCTCGAAACAAAAG
* **
1926033 ATTTTGTCTCACTTGAGACAGTTTTTGCTCGAAACAATAAG
1 ATTTTATCTCACTTGAGACAG-TTTCCCTCGAAACAA-AAG
* ** * * *
1926074 A-TTTATTTCACTCAAGATC-GTTTTTCCTTGAAACATAAG
1 ATTTTATCTCACTTGAGA-CAG-TTTCCCTCGAAACAAAAG
* * * *
1926113 ATTTTATCTCGCTTGAGATAGTTTCCCT--AGA-AATAG
1 ATTTTATCTCACTTGAGACAGTTTCCCTCGAAACAAAAG
* * * *
1926149 -TTTTGTCTCTCTTGAGACAGTTTCCCTAGAAAC--GAG
1 ATTTTATCTCACTTGAGACAGTTTCCCTCGAAACAAAAG
* *
1926185 -TTTTGTCTC-CTTTGAGACAGTTTCCCTTGAAAC--AA-
1 ATTTTATCTCAC-TTGAGACAGTTTCCCTCGAAACAAAAG
* * * *
1926220 ATTTTGTCTCCCTTGAGACGGTTTCCCTTGAAAC--AA-
1 ATTTTATCTCACTTGAGACAGTTTCCCTCGAAACAAAAG
* * * *
1926256 ATTTTATCTCCCTTGAGACAATTTCACTTGAAACAAAAG
1 ATTTTATCTCACTTGAGACAGTTTCCCTCGAAACAAAAG
** * * * *
1926295 ATTTTATCTCGTTTGAGATAGTTTCGCTCGAAACACAAT
1 ATTTTATCTCACTTGAGACAGTTTCCCTCGAAACAAAAG
1926334 ATTTT
1 ATTTT
1926339 TATAAACTAA
Statistics
Matches: 251, Mismatches: 41, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
35 25 0.10
36 98 0.39
37 5 0.02
38 2 0.01
39 65 0.26
40 51 0.20
41 5 0.02
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (39 bp):
ATTTTATCTCACTTGAGACAGTTTCCCTCGAAACAAAAG
Found at i:1926435 original size:43 final size:43
Alignment explanation
Indices: 1926360--1926858 Score: 610
Period size: 43 Copynumber: 11.6 Consensus size: 43
1926350 CCTGATTTTC
* * * *
1926360 AGGGGTTTCTTGATGAAAAGTTTGAAGGACCATCGTGATATGA
1 AGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
* * * *
1926403 AGGGGTTCCTTGATGACAAACTTAAAGAACCATCATGATATGT
1 AGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
* * *
1926446 AGGGGTTCTTTGATGACAAGATTG-AGAAACCATCGTGATATGT
1 AGGGGTTCCTTGATGACAAGCTTGAAG-GACCATCGTGATATGT
* ** * * *
1926489 AGTGGTTTTTTGATGATAAGATTGAAGGACCATCGTGATATGC
1 AGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
* * *
1926532 AGGGGTTGCTTGATAACAAGTTTGAAGGACCATCGTGATATGT
1 AGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
* *
1926575 AGGGGTTCTTTGATGACATGCTTG-AGAGACCATCGTGATATGT
1 AGGGGTTCCTTGATGACAAGCTTGAAG-GACCATCGTGATATGT
* * *
1926618 AGGGGTTTCTTGATGACATGCTTG-AGAGACCATCGCGATATGT
1 AGGGGTTCCTTGATGACAAGCTTGAAG-GACCATCGTGATATGT
* * *
1926661 AGGGGTTTCTTGATGATAAGCTTGAAGGACTATCGTGATATGT
1 AGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
*
1926704 AGGGGGTTCCTTGATGACAAGCTTAAAGGACCATCGTGATATGT
1 A-GGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
* *
1926748 AGGGGTTCTTTGATGACAAGCTTG-AGAAGCCATCGTGATATGT
1 AGGGGTTCCTTGATGACAAGCTTGAAGGA-CCATCGTGATATGT
* * *
1926791 AGGGGTTTCTTGATGAAAAGCTTGAGGGACCATCGTGATATGT
1 AGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
*
1926834 AGGGGTTCCTTGATGACAATCTTGA
1 AGGGGTTCCTTGATGACAAGCTTGA
1926859 TGAACAATTG
Statistics
Matches: 397, Mismatches: 52, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
42 7 0.02
43 345 0.87
44 45 0.11
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (43 bp):
AGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGT
Found at i:1926884 original size:54 final size:54
Alignment explanation
Indices: 1926798--1926907 Score: 168
Period size: 54 Copynumber: 2.0 Consensus size: 54
1926788 TGTAGGGGTT
* *
1926798 TCTTGATGAAAAGCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAA
1 TCTTGATGAAAA-CTTGAGGGACCATCATGATATATAGGGGTTCCTTGATGACAA
*
1926853 TCTTGATGAACAA-TTGAGGGACCATCATGATATATAGGGGTTCCTTGGTGACAA
1 TCTTGATGAA-AACTTGAGGGACCATCATGATATATAGGGGTTCCTTGATGACAA
1926907 T
1 T
1926908 TAAGAAATTG
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
54 39 0.76
55 10 0.20
56 2 0.04
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (54 bp):
TCTTGATGAAAACTTGAGGGACCATCATGATATATAGGGGTTCCTTGATGACAA
Found at i:1927352 original size:3 final size:3
Alignment explanation
Indices: 1927339--1927387 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
1927329 GCTTAAAAAA
* *
1927339 TAT TA- TAT TAT TA- TATT TAT TAT TAT TAA TAT TAT TAG TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
1927383 TAT TA
1 TAT TA
1927388 ATAATAATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.85
4 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1928816 original size:2 final size:2
Alignment explanation
Indices: 1928809--1928849 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1928799 TTACATATTA
*
1928809 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1928850 ATTTATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1931719 original size:2 final size:2
Alignment explanation
Indices: 1931712--1931783 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
1931702 ATCCTTTCAA
1931712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1931754 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1931784 TGAAAGGATA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1932032 original size:23 final size:25
Alignment explanation
Indices: 1931998--1932043 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1931988 TTGACAACAC
1931998 AAAAAAGAAAGAGAGA-AAAAAAGG
1 AAAAAAGAAAGAGAGAGAAAAAAGG
1932022 AAAAAAG-AAGAGAGAGAAAAAA
1 AAAAAAGAAAGAGAGAGAAAAAA
1932044 TAGAGAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (25 bp):
AAAAAAGAAAGAGAGAGAAAAAAGG
Found at i:1932051 original size:27 final size:24
Alignment explanation
Indices: 1931998--1932084 Score: 86
Period size: 25 Copynumber: 3.5 Consensus size: 24
1931988 TTGACAACAC
1931998 AAAAAAGAAAGAGAGAAAAAAAGG
1 AAAAAAGAAAGAGAGAAAAAAAGG
1932022 AAAAAAGAAGAGAGAGAAAAAATAGAG
1 AAAAAAGAA-AGAGAGAAAAAA-AG-G
** * *
1932049 AAAGCA-AAAGAAAAGAAAAGAAGG
1 AAAAAAGAAAG-AGAGAAAAAAAGG
*
1932073 AAAGAAGAAAGA
1 AAAAAAGAAAGA
1932085 AAATCGATCA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
24 16 0.30
25 20 0.38
26 12 0.23
27 5 0.09
ACGTcount: A:0.72, C:0.01, G:0.25, T:0.01
Consensus pattern (24 bp):
AAAAAAGAAAGAGAGAAAAAAAGG
Found at i:1934040 original size:58 final size:54
Alignment explanation
Indices: 1933978--1934148 Score: 172
Period size: 58 Copynumber: 3.1 Consensus size: 54
1933968 TCATTGATAG
1933978 GATGTTTTCAAATGAACTTTTAAAAAGAGAAGCTAAGCCTAATTTTTAGGGGTTTCTT
1 GATGTTTTCAAATGAA-TTTT---AAGAGAAGCTAAGCCTAATTTTTAGGGGTTTCTT
* * * *
1934036 GATGTTTTCAAATGAGTTTT-AGA-AA-CTAAGCCTGATTTTCAGGGGATTCTT
1 GATGTTTTCAAATGAATTTTAAGAGAAGCTAAGCCTAATTTTTAGGGGTTTCTT
*
1934087 GATGATTATTTCCAAA-GAATTTTTTAA-AGAAGCTAAGCCTAATTTTTAGGAGTTTCTT
1 GATG--T-TTT-CAAATGAA--TTTTAAGAGAAGCTAAGCCTAATTTTTAGGGGTTTCTT
1934145 GATG
1 GATG
1934149 ATAACTGAAA
Statistics
Matches: 95, Mismatches: 9, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
51 27 0.28
52 2 0.02
53 4 0.04
54 5 0.05
55 4 0.04
56 5 0.05
57 7 0.07
58 41 0.43
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (54 bp):
GATGTTTTCAAATGAATTTTAAGAGAAGCTAAGCCTAATTTTTAGGGGTTTCTT
Found at i:1934441 original size:39 final size:39
Alignment explanation
Indices: 1934398--1934758 Score: 514
Period size: 39 Copynumber: 9.4 Consensus size: 39
1934388 AGAAATTAAC
1934398 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * * * *
1934437 ATCTCACTTGAGATAGTTTCACTTGAAACGGAAAATTTC
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * *
1934476 ATCTCGTTTGAGATAGTTTCACTTGAAACATAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * * *
1934515 ATTTCGCTTGAGATAGTTTCACTCGGAATAGAATA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1934553 ATCTCGCTTGAGA-AGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
1934591 ATCTCGCTTTAGATAGTTTCACTCGAAACATAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1934629 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
1934668 ATCTGGCTTCAGATAGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * *
1934707 ATCTCACTTAAGATAGTTTCACTCGAAACATAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
1934745 ATCTCACTTGAGAT
1 ATCTCGCTTGAGAT
1934759 TATTTTTCTT
Statistics
Matches: 286, Mismatches: 33, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
37 18 0.06
38 82 0.29
39 186 0.65
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (39 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
Found at i:1934703 original size:22 final size:22
Alignment explanation
Indices: 1934678--1934742 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
1934668 ATCTGGCTTC
*
1934678 AGATAGTTTCACTCGAAACAGA
1 AGATAGTTTCACTCGAAACATA
*
1934700 AGAT--TTT-ATCTC---ACTTA
1 AGATAGTTTCA-CTCGAAACATA
1934717 AGATAGTTTCACTCGAAACATA
1 AGATAGTTTCACTCGAAACATA
1934739 AGAT
1 AGAT
1934743 TTATCTCACT
Statistics
Matches: 33, Mismatches: 3, Indels: 14
0.66 0.06 0.28
Matches are distributed among these distances:
17 7 0.21
19 7 0.21
20 7 0.21
22 12 0.36
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (22 bp):
AGATAGTTTCACTCGAAACATA
Found at i:1934726 original size:192 final size:193
Alignment explanation
Indices: 1934398--1934757 Score: 533
Period size: 192 Copynumber: 1.9 Consensus size: 193
1934388 AGAAATTAAC
*
1934398 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATAGTTTCACTTGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATAGTTTCACTCGA
* * * * * * * *
1934463 AACGGAAAATTTCATCTCGTTTGAGATAGTTTCACTTGAAACATAAGATTTTATTTCGCTTGAGA
66 AACAGAAAATTTCATCTCGCTTCAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTAAGA
* * * *
1934528 TAGTTTCACTCGGAATAGAATATTTATCTCGCTTGAGAAGTTTCACTCGAAACAGAAGATTTT
131 TAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGAAGTTTCACTCGAAACAGAAGATTTT
* * *
1934591 ATCTCGCTTTAGATAGTTTCACTCGAAACATAAGA-TTTATCTCGCTTGAGATAGTTTCACTCGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATAGTTTCACTCGA
* * *
1934655 AACAGAAGATTTTATCTGGCTTCAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTAAGA
66 AACAGAAAATTTCATCTCGCTTCAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTAAGA
*
1934720 TAGTTTCACTCGAAACATAAGATTTATCTCACTTGAGA
131 TAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGA
1934758 TTATTTTTCT
Statistics
Matches: 147, Mismatches: 20, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
192 114 0.78
193 33 0.22
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (193 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATAGTTTCACTCGA
AACAGAAAATTTCATCTCGCTTCAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTAAGA
TAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGAAGTTTCACTCGAAACAGAAGATTTT
Found at i:1934912 original size:59 final size:59
Alignment explanation
Indices: 1934779--1934922 Score: 139
Period size: 59 Copynumber: 2.4 Consensus size: 59
1934769 TAAAAAAACT
* * ** *
1934779 ACGCCTCACTTGAGGGATCAACATTTGCTTTGCTTGATTCACAACATTTTGAATCAGCA
1 ACGCCTCACTTGAGGGATCAACATTTGCTTTGCTCGATTCACAACACTTCAAATCAACA
* * ** * * * *
1934838 ACACCCCACCAGAGGGGTTAACGTTT-CTTTTGCTCGATTCACAACACTTCAAATCAACG
1 ACGCCTCACTTGAGGGATCAACATTTGC-TTTGCTCGATTCACAACACTTCAAATCAACA
1934897 ACGCCTCACTTGAGGGA-CGAACATTT
1 ACGCCTCACTTGAGGGATC-AACATTT
1934923 CCAGTAGAAA
Statistics
Matches: 63, Mismatches: 20, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
58 1 0.02
59 62 0.98
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (59 bp):
ACGCCTCACTTGAGGGATCAACATTTGCTTTGCTCGATTCACAACACTTCAAATCAACA
Found at i:1936238 original size:107 final size:106
Alignment explanation
Indices: 1936079--1936278 Score: 296
Period size: 107 Copynumber: 1.9 Consensus size: 106
1936069 TTTCCCGTGT
** * *
1936079 TTTTACAAAATGGTCACTGTCAGGGACCTTTTTATATTTTCCCAATTTACATGTATGCTTTGTAT
1 TTTTACAAAATAATCACTATCAGGGACCTTTTTATATTTTCCCAATTCACATGTATGCTTTGTAT
1936144 TTTTGGTAAAATATCATTACAGGTCCCCAAACTTTTCTGTG
66 TTTTGGTAAAATATCATTACAGGTCCCCAAACTTTTCTGTG
* *
1936185 TTTTACAAAATAATCACTATCAGTGA-CTATTTTCATAATTTTCTC-ATTCACATGTATGCTTTG
1 TTTTACAAAATAATCACTATCAGGGACCT-TTTT-AT-ATTTTCCCAATTCACATGTATGCTTTG
*
1936248 TATTTTTGGTAAAATATCATTCCAGGTCCCC
63 TATTTTTGGTAAAATATCATTACAGGTCCCC
1936279 CTATGTTTGC
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
105 2 0.02
106 26 0.31
107 49 0.58
108 7 0.08
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (106 bp):
TTTTACAAAATAATCACTATCAGGGACCTTTTTATATTTTCCCAATTCACATGTATGCTTTGTAT
TTTTGGTAAAATATCATTACAGGTCCCCAAACTTTTCTGTG
Found at i:1936386 original size:5 final size:5
Alignment explanation
Indices: 1936344--1936385 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
1936334 TGCAATTTTA
*
1936344 TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTATT TT
1 TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TT
1936386 AATTTAGTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.02, C:0.00, G:0.17, T:0.81
Consensus pattern (5 bp):
TTGTT
Found at i:1936591 original size:11 final size:11
Alignment explanation
Indices: 1936533--1936595 Score: 58
Period size: 11 Copynumber: 5.7 Consensus size: 11
1936523 GTCCTTGTAC
1936533 TTATTTTTATT
1 TTATTTTTATT
*
1936544 CTATTTTTATT
1 TTATTTTTATT
* *
1936555 TTA-TGTTGTT
1 TTATTTTTATT
*
1936565 TTACCTTTTT-TA
1 TTA--TTTTTATT
1936577 TTATTTTTATT
1 TTATTTTTATT
1936588 TTATTTTT
1 TTATTTTT
1936596 TAAAATTAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
10 13 0.32
11 21 0.51
12 4 0.10
13 3 0.07
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:1936943 original size:16 final size:16
Alignment explanation
Indices: 1936919--1936949 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1936909 CTCTTAGAGC
*
1936919 TTGATATTTTAGTCCT
1 TTGACATTTTAGTCCT
1936935 TTGACATTTTAGTCC
1 TTGACATTTTAGTCC
1936950 CTAAACTTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.52
Consensus pattern (16 bp):
TTGACATTTTAGTCCT
Found at i:1938752 original size:22 final size:20
Alignment explanation
Indices: 1938713--1938765 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
1938703 GTTATATTAA
1938713 TAATTATATGTTGAAGATTGGTT
1 TAATTA-ATGTTGAAGATT--TT
1938736 TAATTAATGTT-ATAGATTTT
1 TAATTAATGTTGA-AGATTTT
1938756 T-ATTAATGTT
1 TAATTAATGTT
1938766 TCTTTTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 9 0.31
20 3 0.10
21 1 0.03
22 10 0.34
23 6 0.21
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (20 bp):
TAATTAATGTTGAAGATTTT
Found at i:1938877 original size:49 final size:47
Alignment explanation
Indices: 1938808--1938902 Score: 145
Period size: 49 Copynumber: 2.0 Consensus size: 47
1938798 ATATTAAACG
* *
1938808 ACTTAATACATTAAGAAATCAACCTAAGAAATACTTATATAGAATGTAA
1 ACTTAATAAATTAACAAATCAACCTAAGAAATAC-TAT-TAGAATGTAA
*
1938857 ACTTAATAAATTAACCAATCAACCTAAGAAATACTATTAGAATGTA
1 ACTTAATAAATTAACAAATCAACCTAAGAAATACTATTAGAATGTA
1938903 GCTGGGGATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
47 9 0.21
48 3 0.07
49 31 0.72
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (47 bp):
ACTTAATAAATTAACAAATCAACCTAAGAAATACTATTAGAATGTAA
Found at i:1939822 original size:10 final size:10
Alignment explanation
Indices: 1939809--1939864 Score: 58
Period size: 10 Copynumber: 5.6 Consensus size: 10
1939799 ATAAAAGATC
1939809 GACTCGGGTT
1 GACTCGGGTT
** *
1939819 GACTCGACTC
1 GACTCGGGTT
1939829 GACTCGGGTT
1 GACTCGGGTT
** *
1939839 GACTCGACTC
1 GACTCGGGTT
1939849 GACTCGGGTT
1 GACTCGGGTT
1939859 GACTCG
1 GACTCG
1939865 ACTCGACTCG
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.14, C:0.29, G:0.32, T:0.25
Consensus pattern (10 bp):
GACTCGGGTT
Found at i:1939829 original size:5 final size:5
Alignment explanation
Indices: 1939819--1939875 Score: 60
Period size: 5 Copynumber: 11.4 Consensus size: 5
1939809 GACTCGGGTT
** * ** *
1939819 GACTC GACTC GACTC GGGTT GACTC GACTC GACTC GGGTT GACTC GACTC
1 GACTC GACTC GACTC GACTC GACTC GACTC GACTC GACTC GACTC GACTC
1939869 GACTC GA
1 GACTC GA
1939876 AGTCGAGATC
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.23
Consensus pattern (5 bp):
GACTC
Found at i:1939832 original size:20 final size:20
Alignment explanation
Indices: 1939807--1939874 Score: 136
Period size: 20 Copynumber: 3.4 Consensus size: 20
1939797 CGATAAAAGA
1939807 TCGACTCGGGTTGACTCGAC
1 TCGACTCGGGTTGACTCGAC
1939827 TCGACTCGGGTTGACTCGAC
1 TCGACTCGGGTTGACTCGAC
1939847 TCGACTCGGGTTGACTCGAC
1 TCGACTCGGGTTGACTCGAC
1939867 TCGACTCG
1 TCGACTCG
1939875 AAGTCGAGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.15, C:0.31, G:0.29, T:0.25
Consensus pattern (20 bp):
TCGACTCGGGTTGACTCGAC
Found at i:1952523 original size:3 final size:3
Alignment explanation
Indices: 1952517--1952576 Score: 84
Period size: 3 Copynumber: 19.3 Consensus size: 3
1952507 TTTTTTACCC
* *
1952517 ATT ATT ATT ATT ATA ATT ATT ATT ATT ATA ATT ATT ATAT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T AT-T ATT
1952564 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
1952577 AAAAATAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 45 0.87
4 7 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1965424 original size:23 final size:22
Alignment explanation
Indices: 1965394--1965459 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
1965384 ATATTATACT
1965394 TGAAGAAAAAAAAAGGAAAAAAA
1 TGAAGAAAAAAAAA-GAAAAAAA
*
1965417 TGAAG-AAAGAAAAGAAAAAAA
1 TGAAGAAAAAAAAAGAAAAAAA
*
1965438 -GAAAAAAAAAGAAAAGAAAAAA
1 TG-AAGAAAAA-AAAAGAAAAAA
1965460 GGGGGGTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.03
21 10 0.27
22 10 0.27
23 16 0.43
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (22 bp):
TGAAGAAAAAAAAAGAAAAAAA
Found at i:1965444 original size:15 final size:16
Alignment explanation
Indices: 1965426--1965460 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
1965416 ATGAAGAAAG
1965426 AAAAGAAA-AAAAGAA
1 AAAAGAAAGAAAAGAA
1965441 AAAA-AAAGAAAAGAA
1 AAAAGAAAGAAAAGAA
1965456 AAAAG
1 AAAAG
1965461 GGGGGTCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAGAAAGAAAAGAA
Found at i:1966996 original size:93 final size:92
Alignment explanation
Indices: 1966836--1967174 Score: 534
Period size: 93 Copynumber: 3.6 Consensus size: 92
1966826 ACAAGTGCCA
*
1966836 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTATGAA-CCCAA
*
1966901 AACCCCATCATTGGACTTAAAAGATGAG
65 AACCCCATCATTGGACTTAAAATATGAG
*
1966929 TGTGCTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTATGAACCCTAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTATGAACCC-AA
* *
1966994 AACCCCATCATTAGACTTGAAATATGAG
65 AACCCCATCATTGGACTTAAAATATGAG
*
1967022 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTAGTTTGGTATGAACCACAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTATGAACC-CAA
* * * *
1967087 AAACCAATCATTGGATTTAGAAATATGAA
65 AACCCCATCATTGGACTTA-AAATATGAG
* *
1967116 TGCGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTATGAA
1967175 ACAACAGAAC
Statistics
Matches: 227, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
92 3 0.01
93 159 0.70
94 65 0.29
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Consensus pattern (92 bp):
TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTATGAACCCAAA
ACCCCATCATTGGACTTAAAATATGAG
Found at i:1967153 original size:94 final size:93
Alignment explanation
Indices: 1966835--1967218 Score: 533
Period size: 93 Copynumber: 4.1 Consensus size: 93
1966825 AACAAGTGCC
* *
1966835 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTATGAACCACA
* * *
1966900 AAACCCCATCATTGGACTTAAAAGATGA
66 AAAACCAATCATTGGACTTGAAAGATGA
* *
1966928 GTGTGCTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTATGAACC-CT
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTATGAACCAC-
* * * *
1966992 AAAACCCCATCATTAGACTTGAAATATGA
65 AAAAACCAATCATTGGACTTGAAAGATGA
* *
1967021 GTGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTAGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTATGAACCACA
* *
1967086 AAAACCAATCATTGGATTTAGAAATATGA
66 AAAACCAATCATTGGACTT-GAAAGATGA
* *
1967115 ATGCGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAA--ACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTATGAACCACA
*
1967178 ACAGAACCAATCATT-GAATTGAAAGATGA
66 A-A-AACCAATCATTGGACTTGAAAGATGA
*
1967207 ATGTGATCATAG
1 ATGTGCTCATAG
1967219 TAGAAATAAG
Statistics
Matches: 266, Mismatches: 20, Indels: 11
0.90 0.07 0.04
Matches are distributed among these distances:
92 23 0.09
93 166 0.62
94 77 0.29
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (93 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGTATGAACCACA
AAAACCAATCATTGGACTTGAAAGATGA
Found at i:1968347 original size:113 final size:113
Alignment explanation
Indices: 1968005--1968675 Score: 846
Period size: 113 Copynumber: 6.0 Consensus size: 113
1967995 TAGCAAAGAT
* * ** *
1968005 TCAAATCCATCATTTGA-AGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
*
1968069 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * *
1968117 TTAAATTCATCATTTGATGGATTAACATTGCCA-TGTAGAGTTCATAATGAGAAGAACTCATCAT
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGT-TAGAGTTCATAATGAGAAGAA--C-TCAT
*
1968181 CTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
62 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
1968233 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTTGAGTTCATAATGAGAATAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
1968298 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
1968346 TCAAATCCATCACTTGATGGATCAACTTTTCCAGTTTGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
* *
1968411 AGAAGGAAGAAGAAGTTCATAATGAGAAAAATTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
**
1968459 TCAAATCCATCACTTGATGGATCAGTTTTTCCAG--AGAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGTTAG-AGTTCATAATGAGAAGAACTCATCTG
* ** *
1968522 AAGAA-G-A-AA-AAGTTCACAATGAGAAGAGCTTATTCAACCTTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGC
* ** * * ** *
1968568 AT-AATTTTATCAC---A-GCATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 -TCAAATCCATCACTTGATGGATCAACTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTG
* * ** *
1968628 AAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
1968676 AATGACTCTA
Statistics
Matches: 499, Mismatches: 45, Indels: 33
0.86 0.08 0.06
Matches are distributed among these distances:
105 12 0.02
106 31 0.06
107 1 0.00
108 25 0.05
109 23 0.05
110 31 0.06
111 2 0.00
112 46 0.09
113 226 0.45
114 1 0.00
115 1 0.00
116 99 0.20
117 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAACTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:1968894 original size:3 final size:3
Alignment explanation
Indices: 1968888--1968966 Score: 133
Period size: 3 Copynumber: 26.3 Consensus size: 3
1968878 TTTTTTACCC
1968888 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
1968936 ATA ATT ATT A-T ATAT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT A
1968967 AAAAATAATT
Statistics
Matches: 72, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.03
3 67 0.93
4 3 0.04
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1972750 original size:22 final size:23
Alignment explanation
Indices: 1972724--1972770 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1972714 TCGAAAAGCA
1972724 TGTCA-AAAAACATAAGAAAATG
1 TGTCATAAAAACATAAGAAAATG
* *
1972746 TGTCATAAAAGCATATGAAAATG
1 TGTCATAAAAACATAAGAAAATG
1972769 TG
1 TG
1972771 CAACACAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (23 bp):
TGTCATAAAAACATAAGAAAATG
Found at i:1976462 original size:15 final size:16
Alignment explanation
Indices: 1976442--1976473 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1976432 TGGCAGATCC
1976442 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
1976457 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
1976473 A
1 A
1976474 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:1984240 original size:11 final size:11
Alignment explanation
Indices: 1984206--1984245 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
1984196 ATTTAATAGA
1984206 ATAAATATTAT
1 ATAAATATTAT
1984217 ATAAA-ATTAT
1 ATAAATATTAT
1984227 ATAATATATT-T
1 ATAA-ATATTAT
1984238 AT-AATATT
1 ATAAATATT
1984246 TTTTCAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 5 0.19
10 10 0.37
11 9 0.33
12 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATAAATATTAT
Found at i:1984345 original size:17 final size:17
Alignment explanation
Indices: 1984305--1984347 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1984295 AATTAATAAG
1984305 AAAAAAAATTACAAAGT
1 AAAAAAAATTACAAAGT
* *
1984322 AATAAAAGTTA-AAAGTT
1 AAAAAAAATTACAAAG-T
1984339 AAAAAAAAT
1 AAAAAAAAT
1984348 AAATTGGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (17 bp):
AAAAAAAATTACAAAGT
Found at i:1988790 original size:23 final size:23
Alignment explanation
Indices: 1988755--1988812 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
1988745 TGAATGTTAT
1988755 ATAATAAAATATATATA-AAAATA
1 ATAATAAAATATAT-TACAAAATA
* *
1988778 ATAATATAGTATATTACAAAATTA
1 ATAATAAAATATATTACAAAA-TA
1988802 A-AATTAAAATA
1 ATAA-TAAAATA
1988813 GGTAAACTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
22 2 0.07
23 18 0.64
24 8 0.29
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
ATAATAAAATATATTACAAAATA
Found at i:1990329 original size:6 final size:6
Alignment explanation
Indices: 1990264--1990328 Score: 112
Period size: 6 Copynumber: 10.8 Consensus size: 6
1990254 GATACGTATT
1990264 GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG
1 GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG
* *
1990312 GAAATT GAAATT GAAAT
1 GAAATG GAAATG GAAAT
1990329 TTTAATTGAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.51, C:0.00, G:0.29, T:0.20
Consensus pattern (6 bp):
GAAATG
Found at i:1991283 original size:108 final size:108
Alignment explanation
Indices: 1991084--1991383 Score: 318
Period size: 108 Copynumber: 2.8 Consensus size: 108
1991074 CATCTGTTTA
* * * * * *
1991084 AAGCTGATG-GGGCTTTAAAAATCTGATGATAACAAAATATGTTAAGTACTTAATTTGTTATCAA
1 AAGCTGATGAGGAC-TTAGAAATCTGATGATAACAAAATAGGTTAATTACTTATTTTGTTATAAA
* ***
1991148 TATTATCAACATATTAGGTAGTGCCTAAAATATTACCAAAATTT
65 TATTATCAACATATTAGATAACACCTAAAATATTACCAAAATTT
* * * * *
1991192 AAAAG-T-TTGGGGTCTTAGAAATCCGATGATAACAAAATAGGTTAATTACTTATTTTGTTATTA
1 --AAGCTGATGAGGACTTAGAAATCTGATGATAACAAAATAGGTTAATTACTTATTTTGTTATAA
* * *
1991255 ATATTATCAACATATTAGATAACACCTAAAATGTTGCCAAAGTTT
64 ATATTATCAACATATTAGATAACACCTAAAATATTACCAAAATTT
* * * *
1991300 AAGCTGATGAGGACTTCGAAATTTGACGACAACAAAATAGGTTAATTACTTATTTTGTTATAAAT
1 AAGCTGATGAGGACTTAGAAATCTGATGATAACAAAATAGGTTAATTACTTATTTTGTTATAAAT
* * *
1991365 AAATATTAAAATATTAGAT
66 -ATTATCAACATATTAGAT
1991384 TGCTCCCAAT
Statistics
Matches: 159, Mismatches: 27, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
106 3 0.02
107 1 0.01
108 133 0.84
109 19 0.12
110 3 0.02
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.35
Consensus pattern (108 bp):
AAGCTGATGAGGACTTAGAAATCTGATGATAACAAAATAGGTTAATTACTTATTTTGTTATAAAT
ATTATCAACATATTAGATAACACCTAAAATATTACCAAAATTT
Found at i:1991508 original size:51 final size:51
Alignment explanation
Indices: 1991431--1991528 Score: 178
Period size: 51 Copynumber: 1.9 Consensus size: 51
1991421 TGAAATCTAG
* *
1991431 AATATTAAAGTTGTTTTTAATTATATCAGTAGGATTTAATATATTACCTGA
1 AATATTAAAGTTGTGTTTAATGATATCAGTAGGATTTAATATATTACCTGA
1991482 AATATTAAAGTTGTGTTTAATGATATCAGTAGGATTTAATATATTAC
1 AATATTAAAGTTGTGTTTAATGATATCAGTAGGATTTAATATATTAC
1991529 GTGTCTTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (51 bp):
AATATTAAAGTTGTGTTTAATGATATCAGTAGGATTTAATATATTACCTGA
Found at i:1992110 original size:23 final size:23
Alignment explanation
Indices: 1992075--1992130 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
1992065 GATAACTAGT
* * * *
1992075 TTAATGTAGTAGGTAGCACTTAA
1 TTAACGTAATAGGTAACACATAA
*
1992098 TTAACGTAATAGGTAACACATAT
1 TTAACGTAATAGGTAACACATAA
*
1992121 TTAACATAAT
1 TTAACGTAAT
1992131 CATTAACGCC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (23 bp):
TTAACGTAATAGGTAACACATAA
Found at i:1992225 original size:23 final size:23
Alignment explanation
Indices: 1992195--1992266 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
1992185 CAGTAACTAG
* *
1992195 TTTAATGTAATAGGTATCACTTA
1 TTTAATGTAATAGGTAGCACCTA
* *
1992218 TTTAATGTAATACGTAGCGCCTA
1 TTTAATGTAATAGGTAGCACCTA
** *
1992241 TTTAACATAATAGGTAGCGCCTA
1 TTTAATGTAATAGGTAGCACCTA
1992264 TTT
1 TTT
1992267 TATTTTACCG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (23 bp):
TTTAATGTAATAGGTAGCACCTA
Found at i:1992341 original size:121 final size:122
Alignment explanation
Indices: 1992025--1992333 Score: 410
Period size: 121 Copynumber: 2.6 Consensus size: 122
1992015 AAGTTGTATA
* * * *
1992025 TATTTTACCGTTTACATTATTATTAACTTTTAAACAAATC-GATAACTAGTTTAATGTAGTAGGT
1 TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACCAGGTAACTAGTTTAATGTAATAGGT
* * *
1992089 AGCACTTAATTAACGTAATAGGTAACACATATTTAACATAATCATTAACGCCTATTT
66 AGCACTTATTTAACGTAATACGTAACACATATTTAACATAATCAGTAACGCCTATTT
**
1992146 TATTTTATTGTTTACATTATTATTAACCTTTAAACAAACCA-GTAACTAGTTTAATGTAATAGGT
1 TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACCAGGTAACTAGTTTAATGTAATAGGT
* * * * * *
1992210 ATCACTTATTTAATGTAATACGTAGCGCCTATTTAACATAAT-AGGTAGCGCCTATTT
66 AGCACTTATTTAACGTAATACGTAACACATATTTAACATAATCA-GTAACGCCTATTT
** * *
1992267 TATTTTACCGTTTATGTTATTATTAACCTTTAAACAAA-CAGGTAACTAGTTTAACGTAATAGAT
1 TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACCAGGTAACTAGTTTAATGTAATAGGT
1992331 AGC
66 AGC
1992334 GTTTATTTTA
Statistics
Matches: 163, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
120 3 0.02
121 160 0.98
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (122 bp):
TATTTTACCGTTTACATTATTATTAACCTTTAAACAAACCAGGTAACTAGTTTAATGTAATAGGT
AGCACTTATTTAACGTAATACGTAACACATATTTAACATAATCAGTAACGCCTATTT
Found at i:1992436 original size:149 final size:150
Alignment explanation
Indices: 1992241--1992572 Score: 468
Period size: 149 Copynumber: 2.2 Consensus size: 150
1992231 GTAGCGCCTA
** *
1992241 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTATGTTATTATTAACCTTTAAACAAAC
1 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTACTAACCTTTAAACAAAC
* ** *
1992306 AGGTAACTAGTTTAACGTAATAGATAGCGTTTATTTTATTTTACCGTTTACATTATTAGTAACCT
66 AGATAACTAGTTTAACGTAATAGATAGCGACTATTTTATTTTACCGTTTACATTATTAGTAACAT
* *
1992371 TTAAATAAACCGATAGGTAG
131 TCAAACAAACCGATAGGTAG
* *
1992391 TTTAACCTAATAGGTA-TGCCTATTTTATTTTACCGTTTACATTATTACTAACCTTTAAACAAAC
1 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTACTAACCTTTAAACAAAC
* * * *
1992455 CGATAAGTATTTTAACGTAATAGCTAGCGACTATTTTATTTTACCGTTTACATTATTAGTAACAT
66 AGATAACTAGTTTAACGTAATAGATAGCGACTATTTTATTTTACCGTTTACATTATTAGTAACAT
* *
1992520 TCAAACAAATCGGTAGGTAG
131 TCAAACAAACCGATAGGTAG
* * **
1992540 TTTAATATAATAAGTAGCGAATATTTTATTTTA
1 TTTAACATAATAGGTAGCGCCTATTTTATTTTA
1992573 ACCGGTTAAG
Statistics
Matches: 158, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
149 130 0.82
150 28 0.18
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.41
Consensus pattern (150 bp):
TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTACTAACCTTTAAACAAAC
AGATAACTAGTTTAACGTAATAGATAGCGACTATTTTATTTTACCGTTTACATTATTAGTAACAT
TCAAACAAACCGATAGGTAG
Found at i:1992443 original size:74 final size:74
Alignment explanation
Indices: 1992241--1992572 Score: 396
Period size: 75 Copynumber: 4.4 Consensus size: 74
1992231 GTAGCGCCTA
* ** *
1992241 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTATGTTATTATTAACCTTTAAACAAAC
1 TTTAACGTAATAGGTAGCG-CTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
* * *
1992306 AGGTAACTAG
65 CGATAAGTAG
* * *
1992316 TTTAACGTAATAGATAGCGTTTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAATAAAC
1 TTTAACGTAATAGGTAGCG-CTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
*
1992381 CGATAGGTAG
65 CGATAAGTAG
* *
1992391 TTTAACCTAATAGGTATGC-CTATTTTATTTTACCGTTTACATTATTACTAACCTTTAAACAAAC
1 TTTAACGTAATAGGTA-GCGCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
*
1992455 CGATAAGTAT
65 CGATAAGTAG
* * * *
1992465 TTTAACGTAATAGCTAGCGACTATTTTATTTTACCGTTTACATTATTAGTAACATTCAAACAAAT
1 TTTAACGTAATAGGTAGCG-CTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
* *
1992530 CGGTAGGTAG
65 CGATAAGTAG
** * *
1992540 TTTAATATAATAAGTAGCGAATATTTTATTTTA
1 TTTAACGTAATAGGTAGCG-CTATTTTATTTTA
1992573 ACCGGTTAAG
Statistics
Matches: 221, Mismatches: 33, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
73 2 0.01
74 64 0.29
75 153 0.69
76 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.41
Consensus pattern (74 bp):
TTTAACGTAATAGGTAGCGCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACC
GATAAGTAG
Found at i:1993013 original size:30 final size:29
Alignment explanation
Indices: 1992979--1993043 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
1992969 AAATTTATTG
*
1992979 TATCTATTTGATAAAAGAATTG-AAGTTTAA
1 TATCTA-TT-ATAAAACAATTGAAAGTTTAA
**
1993009 TATCTATTATAAAACTTTTGAAAGTTTAA
1 TATCTATTATAAAACAATTGAAAGTTTAA
1993038 TATCTA
1 TATCTA
1993044 AAAAAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 9 0.29
29 16 0.52
30 6 0.19
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (29 bp):
TATCTATTATAAAACAATTGAAAGTTTAA
Found at i:1998181 original size:100 final size:103
Alignment explanation
Indices: 1997942--1998156 Score: 301
Period size: 107 Copynumber: 2.1 Consensus size: 103
1997932 GTTCATATGG
* * *
1997942 TACCGATACCAAAGATAATGAAAGTATCGATACTCACAAGTTAGTATCGATACTACCAACATTGC
1 TACCGATACCAAAGGTAATGAAAGTATCGATACTCACAAGGTAGTATCGATACT---AACA-TGA
* *
1998007 TCAAATTCCAGAATGCAAAAATGGCACCGATACCCAAAAGGA
62 TCAAATTCCAGAATGCAAAAATGACACCGACACCCAAAAGGA
1998049 TACCGATACCAAAGGTAATGAAAGTATCGATACTCACAAGGTAGTATCGATACT-AC-T-ATCAA
1 TACCGATACCAAAGGTAATGAAAGTATCGATACTCACAAGGTAGTATCGATACTAACATGATCAA
* * *
1998111 ATTCTAGAATGCAAAAATGATACCGACACCCAAAGGGA
66 ATTCCAGAATGCAAAAATGACACCGACACCCAAAAGGA
1998149 TACCGATA
1 TACCGATA
1998157 TTATTTTGTA
Statistics
Matches: 100, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
100 45 0.45
101 1 0.01
103 2 0.02
107 52 0.52
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (103 bp):
TACCGATACCAAAGGTAATGAAAGTATCGATACTCACAAGGTAGTATCGATACTAACATGATCAA
ATTCCAGAATGCAAAAATGACACCGACACCCAAAAGGA
Found at i:1999996 original size:22 final size:22
Alignment explanation
Indices: 1999955--2000021 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
1999945 CTCGTATAAA
1999955 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1999978 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
2000000 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2000022 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:2001756 original size:21 final size:21
Alignment explanation
Indices: 2001732--2001776 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2001722 TCTTGTTCGT
* *
2001732 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2001753 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2001774 TTG
1 TTG
2001777 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2003088 original size:18 final size:16
Alignment explanation
Indices: 2003045--2003091 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
2003035 TTCATTGTAT
2003045 CCTCATTACTTTAATAA
1 CCTCATT-CTTTAATAA
2003062 CC-CATTTCTTATACATAA
1 CCTCA-TTCTT-TA-ATAA
2003080 CCTCATTCTTTA
1 CCTCATTCTTTA
2003092 TCATTCTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 5 0.19
17 8 0.31
18 11 0.42
19 2 0.08
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.43
Consensus pattern (16 bp):
CCTCATTCTTTAATAA
Found at i:2003628 original size:8 final size:8
Alignment explanation
Indices: 2003615--2003640 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2003605 TTCTGACCAT
2003615 ATCTTATA
1 ATCTTATA
2003623 ATCTTATA
1 ATCTTATA
2003631 ATCTTATA
1 ATCTTATA
2003639 AT
1 AT
2003641 TCCAGTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (8 bp):
ATCTTATA
Found at i:2004988 original size:22 final size:22
Alignment explanation
Indices: 2004949--2005013 Score: 112
Period size: 22 Copynumber: 2.9 Consensus size: 22
2004939 CGTATAAATA
2004949 CACCGAAGTGCCCCGTAGAATTG
1 CACCGAAGTG-CCCGTAGAATTG
2004972 CACCGAAGTGCCCGTAGAATTG
1 CACCGAAGTGCCCGTAGAATTG
*
2004994 CACCGTAGTGCCCGTAGAAT
1 CACCGAAGTGCCCGTAGAAT
2005014 GATGTCCATA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
22 31 0.76
23 10 0.24
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (22 bp):
CACCGAAGTGCCCGTAGAATTG
Found at i:2006766 original size:21 final size:21
Alignment explanation
Indices: 2006742--2006786 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2006732 TCTTGTTCGT
* *
2006742 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2006763 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2006784 TTG
1 TTG
2006787 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Done.